2024
An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.
Li C, Bonder M, Syed S, Jensen M, Gerstein M, Zody M, Chaisson M, Talkowski M, Marschall T, Korbel J, Eichler E, Lee C, Shi X. An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Genome Research 2024, 34: 2304-2318. PMID: 39638559, DOI: 10.1101/gr.279419.124.Peer-Reviewed Original ResearchConceptsTopologically associating domainsTopologically associating domains boundariesImpact of structural variantsLymphoblastoid cell linesStructural variantsHuman genomeGene regulationAdjacent TADsHuman lymphoblastoid cell linesCell linesSub-TADGenomic structureInsulate genesChromatin architectureImpact of deletionChromatin structureGenomeAberrant regulationAnalysis pipelineMammalian speciesGenesCCREsFunctional impactChromatinRegulationMassively parallel characterization of regulatory elements in the developing human cortex
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki P, Inoue F, Pereira D, Capauto D, Norton S, Vaccarino F, Pollen A, Nowakowski T, Ahituv N, Pollard K, Akbarian S, Abyzov A, Ahituv N, Arasappan D, Almagro Armenteros J, Beliveau B, Bendl J, Berretta S, Bharadwaj R, Bhattacharya A, Bicks L, Brennand K, Capauto D, Champagne F, Chatterjee T, Chatzinakos C, Chen Y, Chen H, Cheng Y, Cheng L, Chess A, Chien J, Chu Z, Clarke D, Clement A, Collado-Torres L, Cooper G, Crawford G, Dai R, Daskalakis N, Davila-Velderrain J, Deep-Soboslay A, Deng C, DiPietro C, Dracheva S, Drusinsky S, Duan Z, Duong D, Dursun C, Eagles N, Edelstein J, Emani P, Fullard J, Galani K, Galeev T, Gandal M, Gaynor S, Gerstein M, Geschwind D, Girdhar K, Goes F, Greenleaf W, Grundman J, Guo H, Guo Q, Gupta C, Hadas Y, Hallmayer J, Han X, Haroutunian V, Hawken N, He C, Henry E, Hicks S, Ho M, Ho L, Hoffman G, Huang Y, Huuki-Myers L, Hwang A, Hyde T, Iatrou A, Inoue F, Jajoo A, Jensen M, Jiang L, Jin P, Jin T, Jops C, Jourdon A, Kawaguchi R, Kellis M, Khullar S, Kleinman J, Kleopoulos S, Kozlenkov A, Kriegstein A, Kundaje A, Kundu S, Lee C, Lee D, Li J, Li M, Lin X, Liu S, Liu J, Liu J, Liu C, Liu S, Lou S, Loupe J, Lu D, Ma S, Ma L, Margolis M, Mariani J, Martinowich K, Maynard K, Mazariegos S, Meng R, Myers R, Micallef C, Mikhailova T, Ming G, Mohammadi S, Monte E, Montgomery K, Moore J, Moran J, Mukamel E, Nairn A, Nemeroff C, Ni P, Norton S, Nowakowski T, Omberg L, Page S, Park S, Patowary A, Pattni R, Pertea G, Peters M, Phalke N, Pinto D, Pjanic M, Pochareddy S, Pollard K, Pollen A, Pratt H, Przytycki P, Purmann C, Qin Z, Qu P, Quintero D, Raj T, Rajagopalan A, Reach S, Reimonn T, Ressler K, Ross D, Roussos P, Rozowsky J, Ruth M, Ruzicka W, Sanders S, Schneider J, Scuderi S, Sebra R, Sestan N, Seyfried N, Shao Z, Shedd N, Shieh A, Shin J, Skarica M, Snijders C, Song H, State M, Stein J, Steyert M, Subburaju S, Sudhof T, Snyder M, Tao R, Therrien K, Tsai L, Urban A, Vaccarino F, van Bakel H, Vo D, Voloudakis G, Wamsley B, Wang T, Wang S, Wang D, Wang Y, Warrell J, Wei Y, Weimer A, Weinberger D, Wen C, Weng Z, Whalen S, White K, Willsey A, Won H, Wong W, Wu H, Wu F, Wuchty S, Wylie D, Xu S, Yap C, Zeng B, Zhang P, Zhang C, Zhang B, Zhang J, Zhang Y, Zhou X, Ziffra R, Zeier Z, Zintel T. Massively parallel characterization of regulatory elements in the developing human cortex. Science 2024, 384: eadh0559. PMID: 38781390, DOI: 10.1126/science.adh0559.Peer-Reviewed Original ResearchConceptsGene regulatory elementsRegulatory elementsRegulation of enhancer activityCharacterization of regulatory elementsCis-regulatory activityNeuronal developmentPrimary cellsEnhanced activityGene regulationHuman neuronal developmentNucleotide changesEnhancer sequencesSequence basisUpstream regulatorComprehensive catalogHuman cellsDeveloping cortexSequenceVariantsOrganoidsCellsCerebral organoidsCortexHuman cortexNucleotideUsing a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements
Pratt H, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, Consortium P, Gandal M, Geschwind D, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science Advances 2024, 10: eadj4452. PMID: 38781344, PMCID: PMC11114231, DOI: 10.1126/sciadv.adj4452.Peer-Reviewed Original ResearchConceptsEpigenetic dataCell-type-specific gene regulationCis-regulatory elementsComprehensive atlasGenetic variants associated with psychiatric disordersLineage-specific transcription factorsBrain cell typesMammalian elementsPsychENCODE ConsortiumNoncoding regionsEvolutionary historyGene regulationRegulatory elementsSequence mutationsTranscription factorsSequence syntaxRegulatory informationPrimate-specific sequencesBinding sitesHuman traitsCell typesFunctional implicationsPsychiatric disordersSequenceFetal brain development
2020
Data Sanitization to Reduce Private Information Leakage from Functional Genomics
Gürsoy G, Emani P, Brannon CM, Jolanki OA, Harmanci A, Strattan JS, Cherry JM, Miranker AD, Gerstein M. Data Sanitization to Reduce Private Information Leakage from Functional Genomics. Cell 2020, 183: 905-917.e16. PMID: 33186529, PMCID: PMC7672785, DOI: 10.1016/j.cell.2020.09.036.Peer-Reviewed Original ResearchConceptsFunctional genomicsSingle-cell RNA sequencingAccurate reference genomesFunctional genomics datasetsFunctional genomics experimentsOrganismal phenotypesGene regulationReference genomeNext-generation sequencingRaw readsGenomics experimentsRNA sequencingGenomic datasetsGenetic variantsGenomicsKnown individualsSequencingReadsEnvironmental samplesGenomeIlluminaPhenotypeGood statistical powerRegulationStatistical power